Co-reporter:Siddhant Sethi, Yasuharu Takashima, Shigetaka Nakamura, Kenzo Fujimoto
Bioorganic & Medicinal Chemistry Letters 2017 Volume 27, Issue 16(Issue 16) pp:
Publication Date(Web):15 August 2017
DOI:10.1016/j.bmcl.2017.06.042
Genome editing is an important technique for protein engineering, treatment of genetic disorders, and production of non-native proteins. A shortcoming of current enzymatic and chemical methods for genome editing is their limited applicability for in vivo studies. In addition, non-enzymatic methods, such as photochemical DNA editing using 3-cyanovinylcarbazole (CNVK), require high temperatures to affect cytosine to uracil transformations. To overcome this limitation, we developed new photo-cross-linkers based on CNVK, 3-methoxycarbonlycarbazole, 3-carboxyvinylcarbazole, and 3-carbonylamidevinylcarbazole. The use of 3-carboxyvinylcarbazole resulted in greater acceleration of the deamination reaction than that achieved with CNVK. The most likely factors affecting the ability of ultrafast photo-responsive nucleosides to accelerate the deamination reaction are polarity and hydrophilicity of the oligodeoxyribonucleotides that contain photo-cross-linker.Download high-res image (128KB)Download full-size image
Co-reporter:S. Nakamura;H. Yang;C. Hirata;F. Kersaudy;K. Fujimoto
Organic & Biomolecular Chemistry 2017 vol. 15(Issue 24) pp:5109-5111
Publication Date(Web):2017/06/21
DOI:10.1039/C7OB00706J
Various DNA conformational changes are in correlation with biological events. In particular, DNA B–Z equilibrium showed a high correlation with translation and transcription. In this study, we developed a DNA probe containing 5-trifluoromethylcytidine or 5-trifluoromethylthymidine to detect DNA B–Z equilibrium using 19F-NMR. Its probe enabled the quantitative detection of B-, Z-, and ss-DNA based on 19F-NMR chemical shift change.
Co-reporter:Siddhant Sethi;Minako Ooe;Takashi Sakamoto
Molecular BioSystems (2005-Present) 2017 vol. 13(Issue 6) pp:1152-1156
Publication Date(Web):2017/05/30
DOI:10.1039/C7MB00082K
Photo-chemical deamination of cytosine using 3-cyanovinylcarbazole nucleoside (CNVK) mediated photo-cross-linking is a technique for site-directed mutagenesis. Using this technique in vivo requires the elimination of a high-temperature incubation step; instead, incubation should be carried out under physiological conditions. To improve the reactivity of CNVK mediated photo-cross-link induced deamination of cytosine under physiological conditions, an evaluation of base pairing in cytosine was carried out with respect to its deamination. Guanine was replaced with 4 different counter bases (inosine, 2-aminopurine, 5-nitroindole, and nebularine), showing distinct hydrogen bonding patterns with target cytosine, which was incorporated at the −1 position with respect to CNVK in the CNVK-modified photo-responsive oligodeoxyribonucleotides to ascertain the role of hydrogen bonding in deamination under physiological conditions. Among the counter bases, inosine showed the highest acceleration towards the photo-induced deamination reaction.
Co-reporter:Shigetaka Nakamura;Hayato Kawabata
Chemical Communications 2017 vol. 53(Issue 54) pp:7616-7619
Publication Date(Web):2017/07/04
DOI:10.1039/C7CC01746D
In the creation of double duplex formation with genomic DNA, the probe must be able to invade and hybridize to the duplex DNA. We designed new photoresponsive probes containing CNVK and CNU; these probes have a high double-duplex invasion capability upon photoirradiation.
Co-reporter:Dr. Shigetaka Nakamura;Hayato Kawabata ;Dr. Kenzo Fujimoto
ChemBioChem 2016 Volume 17( Issue 16) pp:1499-1503
Publication Date(Web):
DOI:10.1002/cbic.201600236
Abstract
An oligodeoxynucleotide (ODN) containing the ultrafast reversible 3-cyanovinylcarbazole (CNVK) photo-crosslinker was photo-crosslinked to a complementary strand upon exposure to 366 nm irradiation and photosplit by use of 312 nm irradiation. In this paper we report that the photoreaction of CNVK on irradiation at 366 nm involves a photostationary state and that its reaction can be controlled by temperature. Guided by this new insight, we proposed and have now demonstrated previously unknown photosplitting of CNVK aided by DNA strand displacement as an alternative to heating. The photo-crosslinked double-stranded DNA (dsDNA) underwent >80 % photosplitting aided by DNA strand displacement on irradiation at 366 nm without heating. In this photosplitting based on DNA strand displacement, the relative thermal stability of the invader strand with respect to the template strands plays an important role, and an invader strand/template strand system that is more stable than the passenger strand/template strand system induces photosplitting without heating. This new strand-displacement-aided photosplitting occurred in a sequence-specific manner through irradiation at 366 nm in the presence of an invader strand.
Co-reporter:Shigetaka Nakamura and Kenzo Fujimoto
Chemical Communications 2015 vol. 51(Issue 59) pp:11765-11768
Publication Date(Web):29 Apr 2015
DOI:10.1039/C5CC02972D
Photo-cross-linking of trifluorothymidine (TFT) using 3-cyanovinylcarbazole (CNVK) clearly shifted its 19F nuclear magnetic resonance (NMR) signal 8 ppm. This CNVK mediated ultrafast photo-cross-linking-induced shift can be utilized for miRNA detection by hybridization chain reaction (HCR) to detect 10 nM of a target in a sequence-specific manner.
Co-reporter:Takashi Sakamoto, Yuya Tanaka, and Kenzo Fujimoto
Organic Letters 2015 Volume 17(Issue 4) pp:936-939
Publication Date(Web):February 5, 2015
DOI:10.1021/acs.orglett.5b00035
3-Cyanovinylcarbazole modified d-threoninol (CNVD) was incorporated in oligodeoxyribonucleotide and tested for a photo-cross-linking reaction with complementary oligodeoxyribonucleotide. The photoreactivity was 1.8- to 8-fold greater than that of 3-cyanovinylcarbazole modified deoxyribose (CNVK) previously reported. From the results of melting analysis and circular dichroism spectroscopy of the duplexes, the relatively flexible structure of CNVD compared with CNVK might be advantageous for [2 + 2] photocycloaddition between the cyanovinyl group on the CNVD and pyrimidine base in the complementary strand.
Co-reporter:Takashi Sakamoto, Minako Ooe, and Kenzo Fujimoto
Bioconjugate Chemistry 2015 Volume 26(Issue 8) pp:1475
Publication Date(Web):July 18, 2015
DOI:10.1021/acs.bioconjchem.5b00352
To evaluate the effect of base pairing of the target pyrimidine on the interstrand photo-cross-linking reaction of DNA via 3-cyanovinylcarbazole nucleoside (CNVK), a complementary base of target pyrimidine was substituted with noncanonical purine bases or 1,3-propandiol (S). As the decrease of the hydrogen bonds in the base pairing of target C accelerated the photo-cross-linking reaction markedly (3.6- to 7.7-fold), it can be concluded that the number of hydrogen bonds in the base pairing, i.e., the stability of base pairing, of the target pyrimidine plays a critical role in the interstrand photo-cross-linking reaction. In the case of G to S substitution, the highest photoreactivity toward C was observed, whose photoreaction rate constant (k = 2.0 s–1) is comparable to that of CNVK toward T paired with A (k = 3.5 s–1). This is the most reactive photo-cross-linking reaction toward C in the sequence specific interstrand photo-cross-linking. This might facilitate the design of the photo-cross-linkable oligodeoxyribonucleotides for various target sequences.
Co-reporter:Takashi Sakamoto, Atsuo Shigeno, Yuichi Ohtaki and Kenzo Fujimoto
Biomaterials Science 2014 vol. 2(Issue 9) pp:1154-1157
Publication Date(Web):26 Jun 2014
DOI:10.1039/C4BM00117F
3-Cyanovinylcarbazole nucleoside (CNVK), which has an ultrafast photo-cross-linking ability to complementary RNA, was incorporated into the antisense oligonucleotide targeting green fluorescent protein (GFP) mRNA. We successfully demonstrated that the photoreactive antisense oligonucleotides effectively regulate GFP expression in a stable cell line expressing the GFP gene in a photo-responsive manner.
Co-reporter:Shigetaka Nakamura
Journal of Chemical Technology and Biotechnology 2014 Volume 89( Issue 7) pp:1086-1090
Publication Date(Web):
DOI:10.1002/jctb.4205
Abstract
BACKGROUND
The outstanding specificity of the A-T and G-C Watson–Crick hydrogen-bonding interaction allows various DNA nanostructures to be created, which has increased interest in using DNA as a bio- or nano-material. DNA nanostructures have already been used for many applications as well as to create a platform for nanopatterning of a variety of function molecules. However, these structures can be used only at low temperature of Tm value or less in solution because they melt beyond this temperature. This paper reports the creation of a DNA array structure held by photocrosslinking mediated 3-cyanovinylcarbazole (CNVK) which allows crosslinking by photoirradiation in a few seconds.
RESULTS
The thermal stability of DNA nanostructures containing CNVK were evaluated before and after 366 nm UV-exposure by denaturing polyacrylamide gel electrophoresis and the melting curve. When CNVK was arranged in a suitable position into a 2D DNA array, its photocrosslinked structure was stable under denaturing conditions. The solution-state melting profile of the photocrosslinked DNA array was expanded to >80 °C, which is at least a 40 °C increase and showed decreased hyperchromic effect when compared with a non-photocrosslinked structure.
CONCLUSION
The method of creating DNA structures equipped with thermal resistance by ultrafast photocrosslinking reaction provides practical DNA nanodevices and enables the stepwise assembly of DNA structures. © 2013 Society of Chemical Industry
Co-reporter:Kenzo Fujimoto, Yu-ki Takematsu, Atsuo Shigeno, Mirei Furusawa, Takashi Sakamoto
Bioorganic & Medicinal Chemistry Letters 2014 Volume 24(Issue 16) pp:3736-3738
Publication Date(Web):15 August 2014
DOI:10.1016/j.bmcl.2014.07.002
Photo-induced C1′ hydrogen abstraction of 5-fluoro-2′-deoxyuridine was adopted as the key reaction for releasing 5-fluorouracil (5-FU) anticancer drug from oligonucleotide strands. After photoirradiation following 5-FU release, anticancer activity was expected. We demonstrated that oligonucleotide tetramer, d(AFUIUA), can release 5-FU under physiological conditions in a photo-responsive manner thorough photo-induced C1′ hydrogen abstraction, and that the 5-FU released from d(AFUIUA) having a phosphorothioate backbone clearly suppresses the proliferation of HeLa cells in a photo-responsive manner.
Co-reporter:Kenzo Fujimoto ; Asuka Yamada ; Yoshinaga Yoshimura ; Tadashi Tsukaguchi ;Takashi Sakamoto
Journal of the American Chemical Society 2013 Volume 135(Issue 43) pp:16161-16167
Publication Date(Web):October 2, 2013
DOI:10.1021/ja406965f
To clarify the cis–trans isomeric effect on the ultrafast DNA photo-cross-linking reaction of 3-cyanovinylcarbazole nucleoside (CNVK) in the DNA duplex, which gives a single photodimer on the reversed-phase HPLC chromatogram, the kinetics of the cis–trans photoisomerization of CNVK in double-stranded DNA was evaluated. Since the photoisomerization rate constant for cis to trans isomerization in double-stranded DNA was significantly larger than that for trans to cis isomerization, and the thermodynamic stability of the trans isomer was higher than that of the cis isomer, it was strongly suggested that the trans isomer of CNVK is a reactive species of the photo-cross-linking reaction. 1H–1H NOESY analysis of the photoadduct consisting of CNVK and T also supported the trans-mediated photo-cross-linking reaction of CNVK. By using this ultrafast photo-cross-linking reaction for the molecular beacon-based SNPs typing, four individual Japanese rice strains were clearly distinguishable with simple photoirradiation and fluorescence imaging using double-stranded target DNAs.
Co-reporter:Kenzo Fujimoto, Hiroki Yoshinaga, Yasumasa Yoshio and Takashi Sakamoto
Organic & Biomolecular Chemistry 2013 vol. 11(Issue 31) pp:5065-5068
Publication Date(Web):24 May 2013
DOI:10.1039/C3OB40915E
3-Cyanovinylcarbazole nucleoside (CNVK), which can quickly photocrosslink to the pyrimidine base in the DNA double strand, was incorporated into a triplex forming oligonucleotide (TFO). We successfully demonstrated that CNVK in TFO can photocrosslink to the thymine base in Watson–Crick double-stranded DNA via anti-Hoogsteen base pairing with a few seconds of photoirradiation.
Co-reporter:Kenzo Fujimoto;Satomi Kishi;Takashi Sakamoto
Photochemistry and Photobiology 2013 Volume 89( Issue 5) pp:1095-1099
Publication Date(Web):
DOI:10.1111/php.12118
Abstract
To clarify the geometric effect of the ultra-fast photocrosslinking reaction of photoreactive oligodeoxyribonucleotide containing 3-cyanovinylcarbazole nucleoside (CNVK) on uridine in complementary RNA strands, pseudouridine (Ψ), which is an isomer of uridine with a C5–C1′ glycosidic bond, was introduced to the photocrosslink site of CNVK in complementary RNA instead of U. The photoreactivity of CNVK toward Ψ was two-fold lower than that of U, suggesting that the geometry between the vinyl moiety on CNVK and the reactive double bond in the pyrimidine base has a large affect on the photoreactivity of CNVK. Contrary to the case of U, the reactivity of the CNVK toward Ψ was decreased by the decrease of reaction temperature below the Tm of heteroduplex, suggesting that the flexible structure of the duplex is advantageous for the photocrosslinking reaction with Ψ, whose reactive double bond possesses unfavorable geometry for the photocrosslinking reaction with CNVK. These basic findings might contribute to the development of a geometry selective photocrosslinking reaction. This is the first example of a sequence specific photocrosslinking reaction toward Ψ, which is the most abundant posttranscriptionally modified nucleoside.
Co-reporter:Atsuo Shigeno, Takashi Sakamoto, Yoshinaga Yoshimura and Kenzo Fujimoto
Organic & Biomolecular Chemistry 2012 vol. 10(Issue 38) pp:7820-7825
Publication Date(Web):2012/08/08
DOI:10.1039/C2OB25883H
3-Cyanovinylcarbazole nucleoside, which effectively photocrosslinks to the pyrimidine base in complementary RNA strands, was incorporated into antisense oligonucleotides, and we evaluated the photoreactivity and the sequence selectivity to mutated K-ras oligoRNAs, as well as the regulation of the function of K-ras mRNA. We demonstrated that the reverse transcription and the translation activity of K-ras mRNA were quickly suppressed by a few seconds of photoirradiation with the addition of the photoresponsive antisense ODN.
Co-reporter:Kenzo Fujimoto, Kaoru Hiratsuka-Konishi, Takashi Sakamoto, Tomoko Ohtake, Ken-ichi Shinohara and Yoshinaga Yoshimura
Molecular BioSystems 2012 vol. 8(Issue 2) pp:491-494
Publication Date(Web):19 Dec 2011
DOI:10.1039/C2MB05422A
To develop a covalent and specific labeling method for single- and double-stranded plasmid DNA, photoresponsive oligonucleotide containing 3-cyanovinylcarbazole nucleoside was adopted. Single- and double-stranded plasmid DNA was successfully labeled/de-labeled with Cy3 and/or biotin by photoirradiation.
Co-reporter:Takashi Sakamoto, Yu-ki Shimizu, Jun Sasaki, Hikaru Hayakawa, Kenzo Fujimoto
Bioorganic & Medicinal Chemistry Letters 2011 Volume 21(Issue 1) pp:303-306
Publication Date(Web):1 January 2011
DOI:10.1016/j.bmcl.2010.11.013
To image gene expression in vivo, we designed and synthesized a novel signal turn-on probe for 19F nuclear magnetic resonance (MR) imaging based on paramagnetic relaxation enhancement. The stem-loop structured oligodeoxyribonucleotide (ODN) having a molecular beacon sequence for point mutated K-ras mRNA was doubly labeled with bis(trifluoromethyl)benzene moiety and Gd-1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid chelate moiety at the each termini of the ODN probe, respectively. We found that the 19F MR signal of the bis(trifluoromethyl)benzene moiety tethered at the 5′ termini of the probe turned on by the addition of complementary ODN. The probe has the potential to image gene expressions in vivo.
Co-reporter:Kenzo Fujimoto, Kaoru Konishi-Hiratsuka, Takashi Sakamoto and Yoshinaga Yoshimura
Chemical Communications 2010 vol. 46(Issue 40) pp:7545-7547
Publication Date(Web):17 Sep 2010
DOI:10.1039/C0CC03151H
Photo-induced artificial RNA editing was demonstrated using photo-reactive oligonucleotides containing 3-cyanovinylcarbazole nucleoside. This non-enzymatic and sequence-specific methodology will make a major contribution to the elucidation of RNA functions including non-coding RNAs and to the development of drugs based on sequence-specific RNA editing.
Co-reporter:Yoshinaga Yoshimura, Hajime Okada and Kenzo Fujimoto
Organic & Biomolecular Chemistry 2010 vol. 8(Issue 7) pp:1523-1526
Publication Date(Web):17 Feb 2010
DOI:10.1039/B924989C
We describe a photoreversible DNA end capping via 3-cyanovinylcarbazole nucleoside. Doubly end-capped oligodeoxynucleotide (ODN) exhibits increased stability against snake venom phosphodiesterase and shows high thermal stability.
Co-reporter:Kenzo Fujimoto Dr.;Kaoru Konishi-Hiratsuka Dr.;Takashi Sakamoto Dr. ;Yoshinaga Yoshimura Dr.
ChemBioChem 2010 Volume 11( Issue 12) pp:1661-1664
Publication Date(Web):
DOI:10.1002/cbic.201000274
Co-reporter:Masayuki Ogino, Yuuta Taya and Kenzo Fujimoto
Organic & Biomolecular Chemistry 2009 vol. 7(Issue 15) pp:3163-3167
Publication Date(Web):11 Jun 2009
DOI:10.1039/B904941J
We report the nonenzymatic detection of 5-methylcytosine by using template-directed photoligation through 5-vinyl-2′-deoxyuridine derivatives with high selectivity. In this paper, we propose a new detection method by using hydrophobic interaction. The photoligation yield of the 5-methylcytosine case was approximately 5.6-fold higher than that in the case of cytosine.
Co-reporter:Yoshinaga Yoshimura Dr.;Tomoko Ohtake;Hajime Okada Dr.
ChemBioChem 2009 Volume 10( Issue 9) pp:1473-1476
Publication Date(Web):
DOI:10.1002/cbic.200900057
Co-reporter:Masayuki Ogino, Yuuta Taya and Kenzo Fujimoto
Chemical Communications 2008 (Issue 45) pp:5996-5998
Publication Date(Web):14 Oct 2008
DOI:10.1039/B813677G
We report the nonenzymatic detection of 5-methylcytosine by using template-directed photoligation through 5-cyanovinyl-2′-deoxyuridine (CU) with high selectivity and present a new methylation detection method using a photoligation-based DNA chip assay.
Co-reporter:Takehiro Ami Dr.
ChemBioChem 2008 Volume 9( Issue 13) pp:2071-2074
Publication Date(Web):
DOI:10.1002/cbic.200800316
Co-reporter:Kenzo Fujimoto, Shigeo Matsuda, Yoshinaga Yoshimura, Takehiro Ami and Isao Saito
Chemical Communications 2007 (Issue 28) pp:2968-2970
Publication Date(Web):22 Jun 2007
DOI:10.1039/B707524C
We describe a highly efficient method for reversible photocircularization of oligonucleotide (ODN) on a double-stranded DNA template: 5-carboxyvinyl-2′-deoxyuridine-containing ODN was reversibly circularized around the target sequence of the double-stranded plasmid DNA resulting in formation of a catenated plasmid.
Co-reporter:Takehiro Ami, Katsuya Ito, Yoshinaga Yoshimura and Kenzo Fujimoto
Organic & Biomolecular Chemistry 2007 vol. 5(Issue 16) pp:2583-2586
Publication Date(Web):02 Jul 2007
DOI:10.1039/B708264A
We describe a simple and inexpensive SNP typing method by using sequence specific interstrand photocrosslinking via p-carbamoylvinyl phenol nucleosides. Interstrand photocrosslinking showed a high degree of single nucleotide specificity as high as 103-fold and more, and can be used in the diagnostic detection of DNA sequences.
Co-reporter:Yoshinaga Yoshimura, Yuuki Noguchi and Kenzo Fujimoto
Organic & Biomolecular Chemistry 2007 vol. 5(Issue 1) pp:139-142
Publication Date(Web):28 Nov 2006
DOI:10.1039/B615715G
We report the nonenzymatic terminal labeling of oligoribonucleotide (ORN) by using template-directed photoligation through 5-carboxyvinyl-2′-deoxyuridine (CVU) with high selectivity.
Co-reporter:Masayuki Ogino, Daisuke Okamura, Kenzo Fujimoto
Science and Technology of Advanced Materials 2007 Volume 8(Issue 4) pp:318-322
Publication Date(Web):May 2007
DOI:10.1016/j.stam.2007.01.004
We previously reported an efficient and reversible template-directed photoligation using 5-carboxyvinyl-2′-deoxyuridine (CVU)-containing ODN at the 5′-terminal. This method forms d(T-CVU) as a cyclobutane pyrimidine dimer (CPD) analogue between the 3′-terminal thymidine and the 5′-terminal CVU of two oligodeoxynucleotides (ODNs). In this study, we performed PCR using a DNA template containing d(T-CVU). Then, we found that two adenines were incorporated opposite the d(T-CVU).
Co-reporter:Shinzi Ogasawara;Yoshiaki Kyoi Dr.
ChemBioChem 2007 Volume 8(Issue 13) pp:
Publication Date(Web):27 JUL 2007
DOI:10.1002/cbic.200700319
It's logical. We report the development of a photochemical DNA logic systems that performs the basic logic operations NOT, AND and OR, as well as full-adder. In addition, several logic steps can be simultaneously operated in a single test tube by assigning an address sequence to each logic gate (see figure). This approach is generally applicable to the design of other complicated combinational logic circuits, such as comparator and full-subtractor.
Co-reporter:Kenzo Fujimoto, Shigeo Matsuda, Yoshinaga Yoshimura, Takashi Matsumura, Masayuki Hayashi and Isao Saito
Chemical Communications 2006 (Issue 30) pp:3223-3225
Publication Date(Web):21 Jun 2006
DOI:10.1039/B605289D
We report that deamination coupled with 5-carboxyvinyldeoxyuridine-mediated photobranching causes the heat-induced transition of cytosine to uracil with high efficiency without any side reaction.
Co-reporter:Masayuki Ogino Dr.
Angewandte Chemie 2006 Volume 118(Issue 43) pp:
Publication Date(Web):29 SEP 2006
DOI:10.1002/ange.200603161
Ein neues Ende: Zwei nichtmodifizierte Oligodesoxyribonucleotide (ODNs) wurden photochemisch durch das Verändern von ODNs mit photoempfindlichen Nucleosiden an beiden Enden in Gegenwart eines Templat-ODN ligiert. Darüber hinaus wurde die Methode zur Synthese R-förmiger DNA mit einzigartiger Struktur genutzt.
Co-reporter:Shinzi Ogasawara Dr.
Angewandte Chemie 2006 Volume 118(Issue 27) pp:
Publication Date(Web):31 MAY 2006
DOI:10.1002/ange.200600790
Ein Chip für einzelne Fehlpaarungen: Mit einem auf photochemischer Ligation basierenden DNA-Chip zur besseren Unterscheidung von Einzelnucleotidpolymorphismen (siehe Schema) ließ sich zeigen, dass die Reaktion innerhalb von Stunden abläuft, wobei der 50-%-Zustand nach 10 min erreicht ist. Eine einzelne Fehlpaarung in der Zielsequenz führte zu äußerst wenig ligiertem Produkt (103fach geringere Geschwindigkeit als im komplementären Fall).
Co-reporter:Masayuki Ogino Dr.
Angewandte Chemie International Edition 2006 Volume 45(Issue 43) pp:
Publication Date(Web):29 SEP 2006
DOI:10.1002/anie.200603161
Rewriting the end: Two unmodified oligodeoxyribonucleotides (ODNs) were photochemically ligated through modification of ODNs that contain photosensitive nucleosides at both terminal ends in the presence of a template ODN. Additionally, this method was applied to the synthesis of R-shaped DNA as a unique structure.
Co-reporter:Shinzi Ogasawara Dr.
Angewandte Chemie International Edition 2006 Volume 45(Issue 27) pp:
Publication Date(Web):31 MAY 2006
DOI:10.1002/anie.200600790
A chip for single mismatches: Results obtained with a photochemical-ligation-based DNA chip for enhanced discrimination of single-nucleotide polymorphisms (see scheme) show that the reaction takes place over a period of hours, with the 50 % stage reached within 10 minutes. A single mismatch in the target sequence yielded extremely little ligated product (a rate 103-fold lower than for the complementary case).
Co-reporter:Yoshinaga Yoshimura Dr.;Yuuki Noguchi Dr.;Hideaki Sato Dr.
ChemBioChem 2006 Volume 7(Issue 4) pp:
Publication Date(Web):27 FEB 2006
DOI:10.1002/cbic.200500534
Spotlight on RNA sequences. Efficient photoligation, without any by-product formation, was observed when a carboxyvinyl-2′-deoxyuridine-containing oligodeoxynucleotide was photoirradiated with one containing a pyrimidine base at the 3′ end in the presence of template RNA. Furthermore, RNA mismatches can be successfully distinguished by using a DNA-chip assay based on this photoligation. Therefore, this system could be widely used for the detection of RNA sequences.
Co-reporter:Kenzo Fujimoto, Yoshinaga Yoshimura, Tadayoshi Ikemoto, Akio Nakazawa, Masayuki Hayashi and Isao Saito
Chemical Communications 2005 (Issue 25) pp:3177-3179
Publication Date(Web):24 May 2005
DOI:10.1039/B504162G
A modified oligodeoxynucleotide (ODN) containing N3-methyl-5-cyanovinyl-2′-deoxyuridine reacts by photoirradiation at 366 nm with an adenine residue of a complementary template ODN to yield an end-capped ODN in 87% yield.
Co-reporter:Shinzi Ogasawara Assoc. Dr.
ChemBioChem 2005 Volume 6(Issue 10) pp:
Publication Date(Web):12 SEP 2005
DOI:10.1002/cbic.200500188
Branching out into the nano world. We have demonstrated that DNA containing 5-carboxyvinyldeoxyuridine (CVU) at midstream can be used to synthesize multiple-branched DNA with high efficiency by irradiation at 366 nm (see scheme). This novel method is well suited to DNA nanodevices such as the DNA walker, DNA computer, and DNA architecture, as well as to signal amplification.
Co-reporter:S. Nakamura, H. Yang, C. Hirata, F. Kersaudy and K. Fujimoto
Organic & Biomolecular Chemistry 2017 - vol. 15(Issue 24) pp:NaN5111-5111
Publication Date(Web):2017/04/20
DOI:10.1039/C7OB00706J
Various DNA conformational changes are in correlation with biological events. In particular, DNA B–Z equilibrium showed a high correlation with translation and transcription. In this study, we developed a DNA probe containing 5-trifluoromethylcytidine or 5-trifluoromethylthymidine to detect DNA B–Z equilibrium using 19F-NMR. Its probe enabled the quantitative detection of B-, Z-, and ss-DNA based on 19F-NMR chemical shift change.
Co-reporter:Shigetaka Nakamura and Kenzo Fujimoto
Chemical Communications 2015 - vol. 51(Issue 59) pp:NaN11768-11768
Publication Date(Web):2015/04/29
DOI:10.1039/C5CC02972D
Photo-cross-linking of trifluorothymidine (TFT) using 3-cyanovinylcarbazole (CNVK) clearly shifted its 19F nuclear magnetic resonance (NMR) signal 8 ppm. This CNVK mediated ultrafast photo-cross-linking-induced shift can be utilized for miRNA detection by hybridization chain reaction (HCR) to detect 10 nM of a target in a sequence-specific manner.
Co-reporter:Masayuki Ogino, Yuuta Taya and Kenzo Fujimoto
Chemical Communications 2008(Issue 45) pp:NaN5998-5998
Publication Date(Web):2008/10/14
DOI:10.1039/B813677G
We report the nonenzymatic detection of 5-methylcytosine by using template-directed photoligation through 5-cyanovinyl-2′-deoxyuridine (CU) with high selectivity and present a new methylation detection method using a photoligation-based DNA chip assay.
Co-reporter:Kenzo Fujimoto, Kaoru Konishi-Hiratsuka, Takashi Sakamoto and Yoshinaga Yoshimura
Chemical Communications 2010 - vol. 46(Issue 40) pp:NaN7547-7547
Publication Date(Web):2010/09/17
DOI:10.1039/C0CC03151H
Photo-induced artificial RNA editing was demonstrated using photo-reactive oligonucleotides containing 3-cyanovinylcarbazole nucleoside. This non-enzymatic and sequence-specific methodology will make a major contribution to the elucidation of RNA functions including non-coding RNAs and to the development of drugs based on sequence-specific RNA editing.
Co-reporter:Takehiro Ami, Katsuya Ito, Yoshinaga Yoshimura and Kenzo Fujimoto
Organic & Biomolecular Chemistry 2007 - vol. 5(Issue 16) pp:NaN2586-2586
Publication Date(Web):2007/07/02
DOI:10.1039/B708264A
We describe a simple and inexpensive SNP typing method by using sequence specific interstrand photocrosslinking via p-carbamoylvinyl phenol nucleosides. Interstrand photocrosslinking showed a high degree of single nucleotide specificity as high as 103-fold and more, and can be used in the diagnostic detection of DNA sequences.
Co-reporter:Yoshinaga Yoshimura, Hajime Okada and Kenzo Fujimoto
Organic & Biomolecular Chemistry 2010 - vol. 8(Issue 7) pp:NaN1526-1526
Publication Date(Web):2010/02/17
DOI:10.1039/B924989C
We describe a photoreversible DNA end capping via 3-cyanovinylcarbazole nucleoside. Doubly end-capped oligodeoxynucleotide (ODN) exhibits increased stability against snake venom phosphodiesterase and shows high thermal stability.
Co-reporter:Yoshinaga Yoshimura, Yuuki Noguchi and Kenzo Fujimoto
Organic & Biomolecular Chemistry 2007 - vol. 5(Issue 1) pp:NaN142-142
Publication Date(Web):2006/11/28
DOI:10.1039/B615715G
We report the nonenzymatic terminal labeling of oligoribonucleotide (ORN) by using template-directed photoligation through 5-carboxyvinyl-2′-deoxyuridine (CVU) with high selectivity.
Co-reporter:Masayuki Ogino, Yuuta Taya and Kenzo Fujimoto
Organic & Biomolecular Chemistry 2009 - vol. 7(Issue 15) pp:NaN3167-3167
Publication Date(Web):2009/06/11
DOI:10.1039/B904941J
We report the nonenzymatic detection of 5-methylcytosine by using template-directed photoligation through 5-vinyl-2′-deoxyuridine derivatives with high selectivity. In this paper, we propose a new detection method by using hydrophobic interaction. The photoligation yield of the 5-methylcytosine case was approximately 5.6-fold higher than that in the case of cytosine.
Co-reporter:Kenzo Fujimoto, Hiroki Yoshinaga, Yasumasa Yoshio and Takashi Sakamoto
Organic & Biomolecular Chemistry 2013 - vol. 11(Issue 31) pp:NaN5068-5068
Publication Date(Web):2013/05/24
DOI:10.1039/C3OB40915E
3-Cyanovinylcarbazole nucleoside (CNVK), which can quickly photocrosslink to the pyrimidine base in the DNA double strand, was incorporated into a triplex forming oligonucleotide (TFO). We successfully demonstrated that CNVK in TFO can photocrosslink to the thymine base in Watson–Crick double-stranded DNA via anti-Hoogsteen base pairing with a few seconds of photoirradiation.
Co-reporter:Atsuo Shigeno, Takashi Sakamoto, Yoshinaga Yoshimura and Kenzo Fujimoto
Organic & Biomolecular Chemistry 2012 - vol. 10(Issue 38) pp:NaN7825-7825
Publication Date(Web):2012/08/08
DOI:10.1039/C2OB25883H
3-Cyanovinylcarbazole nucleoside, which effectively photocrosslinks to the pyrimidine base in complementary RNA strands, was incorporated into antisense oligonucleotides, and we evaluated the photoreactivity and the sequence selectivity to mutated K-ras oligoRNAs, as well as the regulation of the function of K-ras mRNA. We demonstrated that the reverse transcription and the translation activity of K-ras mRNA were quickly suppressed by a few seconds of photoirradiation with the addition of the photoresponsive antisense ODN.
Co-reporter:Kenzo Fujimoto, Shigeo Matsuda, Yoshinaga Yoshimura, Takehiro Ami and Isao Saito
Chemical Communications 2007(Issue 28) pp:NaN2970-2970
Publication Date(Web):2007/06/22
DOI:10.1039/B707524C
We describe a highly efficient method for reversible photocircularization of oligonucleotide (ODN) on a double-stranded DNA template: 5-carboxyvinyl-2′-deoxyuridine-containing ODN was reversibly circularized around the target sequence of the double-stranded plasmid DNA resulting in formation of a catenated plasmid.
Co-reporter:Takashi Sakamoto, Atsuo Shigeno, Yuichi Ohtaki and Kenzo Fujimoto
Biomaterials Science (2013-Present) 2014 - vol. 2(Issue 9) pp:NaN1157-1157
Publication Date(Web):2014/06/26
DOI:10.1039/C4BM00117F
3-Cyanovinylcarbazole nucleoside (CNVK), which has an ultrafast photo-cross-linking ability to complementary RNA, was incorporated into the antisense oligonucleotide targeting green fluorescent protein (GFP) mRNA. We successfully demonstrated that the photoreactive antisense oligonucleotides effectively regulate GFP expression in a stable cell line expressing the GFP gene in a photo-responsive manner.
Co-reporter:Shigetaka Nakamura, Hayato Kawabata and Kenzo Fujimoto
Chemical Communications 2017 - vol. 53(Issue 54) pp:NaN7619-7619
Publication Date(Web):2017/06/15
DOI:10.1039/C7CC01746D
In the creation of double duplex formation with genomic DNA, the probe must be able to invade and hybridize to the duplex DNA. We designed new photoresponsive probes containing CNVK and CNU; these probes have a high double-duplex invasion capability upon photoirradiation.
![Phenol,4-[5-(4-methyl-1-piperazinyl)[2,5'-bi-1H-benzimidazol]-2'-yl]-](http://img.cochemist.com/ccimg/23500/23491-44-3.png)
![Phenol,4-[5-(4-methyl-1-piperazinyl)[2,5'-bi-1H-benzimidazol]-2'-yl]-](http://img.cochemist.com/ccimg/23500/23491-44-3_b.png)